Accurately evaluating the health state of tunnel structure is of great significance for ensuring the operation safety of tunnel. Based on engineering investigation, fuzzy mathematics and statistical analysis, this paper proposes a new method to evaluate the health state of highway tunnel structure, which considers the multi-disease characteristics and adaptive comprehensive weighting theory. Firstly, by investigating the health state of 20 operation highway tunnels in China, a tunnel disease database with 539 samples was constructed. Considering some new tunnel diseases such as floor heave and lining spalling, a health evaluation index system of highway tunnel was established further. Secondly, utilizing the subjective-objective weighting theory and the principle of variable weight, a new adaptive comprehensive weighting method was proposed to calculate the indexes’ weights. This method overcomes the defect that the constant weight cannot be dynamically updated according to the actual situation of disease development. Then, according to the established four-level classification standard suitable for health evaluation of highway tunnels, the normal distribution membership functions of second-level indexes were determined. Combining with the fuzzy theory, the quantitative evaluation model of tunnel health state was constructed further, which was applied to a case study of the Nanyangshan Tunnel of Kanglin Expressway in China. Furthermore, a comparative analysis with the traditional subjective-objective combination weighting method was conducted, demonstrating the advantages of the proposed evaluation method in terms of engineering applicability and result accuracy. The research findings can provide a decision-making basis for the health maintenance and scientific management of highway tunnels in China.